The Lewis rat, an inbred rat strain susceptible to several well-characterized experimental autoimmune diseases, provides a good model to study peptide-mediated immunotherapy. Peptide immunotherapy focussing on the modulation of T cell responses by interfering with TCR–peptide– MHC complex formation requires the elucidation of the molecular basis of TCR–peptide–MHC interactions for an efficient design of modulatory peptides. In the Lewis rat most autoimmuneassociated CD4F T cell responses are MHC class II RT1.BL restricted. In this study, the characteristics of RT1.BL–peptide interactions were explored. A series of substitution analogs of two Lewis rat T cell epitopes was examined in a direct peptide–MHC binding assay on isolated RT1.BL molecules. Furthermore, other autoimmune-related as well as non-disease-related T cell epitopes were tested in the binding assay. This has led to the definition of an extended RT1.BL– peptide binding motif. The RT1.BL–peptide binding motif established in this study is the first described rat MHC–peptide binding motif based on direct MHC–peptide binding experiments. To predict good or intermediate RT1.BL binding peptides, T cell epitope search profiles were deduced from this motif. The motif and search profiles will greatly facilitate the prediction of modulatory peptides based on autoimmune-associated T cell epitopes and the identification of target structures in experimental autoimmune diseases in Lewis rats.
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